The DNA Sequencing Core will support the needs of RCE projects for large-scale DNA analysis. Three projects are principally dependent on this Core: the Human Innate Immunity Variation Project, the Essential and Virulence Gene Project, and the Bacterial Diversity Project. Most of the activity will involve DNA sequencing either of bacterial genomes, fosmid clones derived from bacterial genomes, PCR products amplified from human subjects, and PCR products amplified from the boundaries of transposon insertions into bacterial genomes. The Core is organized as a "virtual core" within the University of Washington Genome Center (UWGC), which has experience with high-throughput implementation of all the relevant techniques. With this organization, the Core can benefit from the UWGC's infrastructure, management system, and the prorated contributions of a larger and more experienced staff than could be supported by the RCE alone. Most of the techniques are standard. The emphasis is on dye-terminator sequencing on commercial, 96-capillary sequencing instruments. Robots are used extensively to prepare samples, which are processed in 96- or 384-well microtiter plates. An established laboratory-information-management system provides sample tracking and quality-control reports on all activities. For data analysis, there is a major reliance on the phred/phrap/consed software package for processing high-throughput DNA sequencing data. The main activity other than DNA sequencing is the high-throughput fingerprinting of fosmid clones by digestion with restriction enzymes. For this purpose, 96-well processing of samples, high-lane densities on agarose gels, and quantitative image analysis will be employed.